RetrogeneDB ID: retro_mmus_3663

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:94772618..94774034(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082776
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: U2af2
• Ensembl ID: ENSMUSG00000030435
• Aliases: U2af2, 65kDa
• Description: U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2 [Source:MGI Symbol;Acc:MGI:98886]

Sequence

>retro_mmus_3663
ATGTCGGACTTCTACAAGTTTGAGCAGCAGCTCAAGGGGAACAAAGAAGAACGGGACAAGGAGAACCGGCACCATAAGCG
TAGTCACAGTCGCTCTCGAAGCCGAGATAGAAAGCGCAGGAGCTGGAGCCGAGAGCGGCGCAATCCAGACCAGCGCAGTG
ACTCTCAGGATAGGAGGCGGCGACGACGAAGCCAACATTTGACCAGAGGCGCTAAAGAGGAGCAGGGTGGATGGATTCGT
TCCCCGTGCCATGAGAAGAAGAAGGTGCGTAAATACTGGGACGTGCCGCCACCTGGCTTTGAGCACGTCACCCCAATGCA
GTACAAGGCCATGCAAGCTGCTGGTCAGATTCTAGCCACCGCCCTTCTCCCGACCATGACTCCTGGTGGTCTGGCTGTGA
CCCCGATGCCAGTGCCTGTGGTTGGGAGCCAGATGACCAGACAGGCCAGACGTCTCTACGTGGGCACCATCCCTTTTGGC
ATCACCGAGGAGTCTATGCTGGACTTCTTAAACACCCAGATGCATCTGAGGGGCTTGACTCAGGCCCCTGGCAACCCGAT
CTTGGCTGTGCAGATAAATCTAGACAAAAATTTTGCTTTTTTGGAGTTCCGGTCAGTGGATGAGACGACCCAGGCCTTGG
CCTTTGATGGCATCATCTTCCAGGGCCAGTCATTGAAGATTCGAAGGCCTCATGACTACCAACCACTGCCTGGCATGTCA
GGGAGCCCCTCTGTTTATGTGCCTGGAGTTGTATCCACCATAGTCCCAGACTCTGCCCACAAGCTGTTCATCGGGGGTTT
GCCCAACTACCTAAATGATGACCAGGTAAAAGAGCTGCTGACATCCGTTGGGATTCTCAGGGCCTTCAACTTGGTCAAGG
ATAGTATCACAGGGCTCTCCAAGGGCTATGCCTTCTGTGAGTACATGGACATCAACGTCACCGATCAGGCCATTGCGTGG
CTGAATGGGATGCATCTAGGGGACAAGAAGCTGCTTGTCCAGAGGGCAAGTGTGGGAGCCAAGAATGTCGCTCTGAGCAT
CATCAATCAGACACCTGTGACCCTTCAAGTGCCCGGCCTGACGAGCTCTCAGGTGCAGATGGGCGGTCACCCAACTACGG
TCCTGTGCCTCATGAACATGGTGCTCCCCAAGGAGCTGCTGGACGACGAGGAATATGAAGAGATTGTAGACGACGTACGA
GACGAGTGCAACAAGTATGGACTGGTCAAATCGATTGAAATTCCCCGCCCCATGGATGGTGTTGAGGTGCCTGGCTGTGG
AAAGATCTTTGTGGAGTTCACTTCTGTGATTGACTGCCAGAAAGCTATGCAGGGTCTAACTGGCCGCAAGTTCGCCAACA
GAGTGGTGGTCACCAAATACTGTGACCCTGACTCTTACCACGGTCGGAACTTCTGG

Alignment

ORF - retro_mmus_3663 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDFDEFERQLNENKQERDKENRHRKRSHSRSRSRDRKRRSRSRDRRNRDQRSASRDRRRR--SKPLTRG
          MSDF..FE.QL..NK.ERDKENRH.KRSHSRSRSRDRKRRS.SR.RRN.DQRS.S.DRRRR..S..LTRG
Retrocopy MSDFYKFEQQLKGNKEERDKENRHHKRSHSRSRSRDRKRRSWSRERRNPDQRSDSQDRRRRRRSQHLTRG

Parental  AKEEHGGLIRSPRHEKKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMTPDGLAVTPTPVP
          AKEE.GG.IRSP.HEKKK.VRKYWDVPPPGFEH.TPMQYKAMQAAGQI.ATALLPTMTP.GLAVTP.PVP
Retrocopy AKEEQGGWIRSPCHEKKK-VRKYWDVPPPGFEHVTPMQYKAMQAAGQILATALLPTMTPGGLAVTPMPVP

Parental  VVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET
          VVGSQMTRQARRLYVG.IPFGITEE.M.DF.N.QM.L.GLTQAPGNP.LAVQIN.DKNFAFLEFRSVDET
Retrocopy VVGSQMTRQARRLYVGTIPFGITEESMLDFLNTQMHLRGLTQAPGNPILAVQINLDKNFAFLEFRSVDET

Parental  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKEL
          TQA.AFDGIIFQGQSLKIRRPHDYQPLPGMS..PSVYVPGVVST.VPDSAHKLFIGGLPNYLNDDQVKEL
Retrocopy TQALAFDGIIFQGQSLKIRRPHDYQPLPGMSGSPSVYVPGVVSTIVPDSAHKLFIGGLPNYLNDDQVKEL

Parental  LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATLVSLP
          LTS.G.L.AFNLVKDS.TGLSKGYAFCEY.DINVTDQAIA.LNGM.LGDKKLLVQRASVGAKN..L....
Retrocopy LTSVGILRAFNLVKDSITGLSKGYAFCEYMDINVTDQAIAWLNGMHLGDKKLLVQRASVGAKNVAL----

Parental  STINQTPVTLQVPGLMSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIP
          S.INQTPVTLQVPGL.SSQVQMGGHPT.VLCLMNMVLP.ELLDDEEYEEIV.DVRDEC.KYGLVKSIEIP
Retrocopy SIINQTPVTLQVPGLTSSQVQMGGHPTTVLCLMNMVLPKELLDDEEYEEIVDDVRDECNKYGLVKSIEIP

Parental  RPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDFW
          RP.DGVEVPGCGKIFVEFTSV.DCQKAMQGLTGRKFANRVVVTKYCDPDSYH.R.FW
Retrocopy RPMDGVEVPGCGKIFVEFTSVIDCQKAMQGLTGRKFANRVVVTKYCDPDSYHGRNFW

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	1.68 RPM	72.96 RPM
SRP007412_cerebellum	0.35 RPM	76.86 RPM
SRP007412_heart	0.22 RPM	54.70 RPM
SRP007412_kidney	0.37 RPM	63.72 RPM
SRP007412_liver	0.11 RPM	43.15 RPM
SRP007412_testis	0.41 RPM	51.69 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3663 was not detected

EST

No EST(s) were mapped for retro_mmus_3663 retrocopy.

TSS

No TSS is located nearby retro_mmus_3663 retrocopy 5' end.

Lab

retro_mmus_3663 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3663 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000018056	1 retrocopy	retro_lafr_94,
Myotis lucifugus	ENSMLUG00000011051	2 retrocopies	retro_mluc_406, retro_mluc_797,
Macaca mulatta	ENSMMUG00000004810	1 retrocopy	retro_mmul_30,
Mus musculus	ENSMUSG00000030435	3 retrocopies	retro_mmus_2251, retro_mmus_3663 , retro_mmus_991,
Otolemur garnettii	ENSOGAG00000007206	1 retrocopy	retro_ogar_3304,